Microbial Genetics, Genomics, and Bioinformatics
My research interests are in bacterial cell-cycle regulation, role of gene duplication in metabolic innovations, and evolution of genomic complexity in prokaryotes. Rhodobacter sphaeroides, a member of α-3 Proteobacteria, is a model organism for these investigations in my laboratory. R. sphaeroides possesses a complex genome structure, including multiple chromosomes and abundance of duplicated genes, and it also exhibits a great repertoire of metabolic capabilities.
Bacterial cell cycle involves DNA replication, chromosome segregation, and septum formation (cytokinesis). These molecular and cellular processes are coordinated and controlled by regulatory networks. Since prokaryotic cells lack mitosis-like apparatus, multiple chromosomes in bacteria pose a considerable problem for the coordinated replication and the accurate segregation of the chromosomes. To understand the behavior of two chromosomes throughout cell cycle in R. sphaeroides, cloned origins of replication from two chromosomes is being investigated for their replication and cellular localization. Different genetic, biochemical, and bioinformatic methods are employed for this investigation.
The genome of R. sphaeroides contains ~29% of gene duplications, and its roles have been implicated in evolutionary novelties for genome and organismic evolution. We are interested how do different structural and functional constraints of duplicate copies of each gene-pair affect their mRNA expression. This study utilizes both bioinformatic and molecular approaches, such as Ka/Ks estimates, phylogenetic tree construction, and microarray expression analysis.
We are also interested in origin and evolution of genome complexity in bacteria. We performed genome analyses on bacterial species, which possess multiple chromosomes, and have conclusively demonstrated the ancient origin of second chromosome. Since the second chromosome rapidly evolved, we want to investigate further whether second chromosome has specialized role or has evolved to a level where it has become important for the organism in all growth conditions.
- Bacterial cell-cycle regulation
- Genetic and evolutionary analyses of duplicate genes
- Analysis of chromosomal origin of replication
- Analysis of genome complexity: Evolution of complex bacterial genomes
Madhusudan Choudhary, Hyuk Cho, Anish Bavishi, Cheramie Trahan, and Bat-Erdene Myagmarjav (2012) Evolution of Multipartite Genomes in Prokaryotes. In Evolutionary Biology: Mechanisms and Trend, Pierre Pontarotti (eds.), pp 301-323, Springer Verlag Inc. ISBN 978-3-642-30424-8. pdf
Abhishek, Ankur, Anish Bavishi, Ashay Bavishi, and M. Choudhary (2011) Bacterial Chimaerism and the Origin of Mitochondria. Can. J. Microbiol. 57 (1): 49-61. pdf
Bavishi, Anish, Lin Lin, Kristen Schroeder, Anne Peters, Hyuk Cho, and M. Choudhary (2010) Prevalence of gene duplications and their ancient origin in Rhodobacter sphaeroides 2.4.1. BMC Microbiology, 10: 331. pdf
Bavishi, Anish, Ankur Abhishek, Lin Lin, and Madhusudan Choudhary (2010) Complex Prokaryotic Genome Structure: rapid Evolution of CII. Genome Volume 53 (9): 675-687. pdf
Mackenzie, C., Eraso, J., Choudhary, M., Roh, J., Zeng, X., Bruscella P., Puskas, A., and Kaplan, S. (2007) Post-Genomic Adventures with Rhodobacter sphaeroides. Annu. Rev. Microbiol., 61: 283-307. pdf
Choudhary, M., Zanhua, X., Fu, Y. X., and Kaplan, S. (2007) Genome analysis of three strains of Rhodobacter sphaeroides: Evidence of rapid evolution of CII. J. Bacteriology, 189: 1914-1921. pdf
Chris Mackenzie, Madhusudan Choudhary, Frank W. Larimer, Paul F. Predki, Stephanie Stilwagen, Judith P. Armitage, Robert D. Barber, Timothy J. Donohue, Jonathan P. Hosler, Jack E. Newman, James P. Shapleigh, R. Elizabeth Sockett, Jill Zeilstra-Ryalls and Samuel Kaplan (2001) The home stretch, a first analysis of the nearly completed genome of Rhodobacter sphaeroides 2.4.1, Photosynthesis Research 70: 19–41. pdf